Neanderthal admixture & the ecology of academe

By Razib Khan | August 14, 2012 11:02 pm

Yesterday I pointed out that David Reich had a moderately dismissive attitude toward the new paper in PNAS, Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Here’s what Reich said:

…But Reich believes that the discussion would have been different if it had happened in the open. The PNAS paper questioning the Neanderthal admixture addresses issues swirling around two years ago, but not Reich and Slatkin’s latest work. “It’s been an issue for several years. They were right to work on this,” says Reich. But now, “it’s kind of an obsolete paper,” he says.

Here’s what Nick Patterson, Reich’s colleague told me via email:

Ancient structure in Africa was considered when we wrote the Green et al. paper, and we were aware that this could explain D-statistics. But the hypothesis is no longer viable as the major explanation of Neandertal genetics in Eurasia. This was discussed in the recent paper of Yang et al. (MBE, 2012). (Not referenced by the PNAS paper).

A very simple argument, that convinces me, is that the allelic frequency spectrum of Neandertal alleles in Eurasia falls off very quickly. A bottleneck flattens out the spectrum, and it turns out that the Neandertal gene flow has to be placed after the out of Africa bottleneck or the spectrum is much too flat.

The paper on the arXiv from the Reich lab (Sankararaman et al.) is trying to do something much more subtle than this and date the flow. I personally am no longer interested in explaining the introgression as ancient structure. That ship has sailed.

Of course the question of what was the genetic structure of Ancient Africa is quite open, and remains very interesting.

If Nick’s explanation is a bit cryptic for you (he was a cryptographer!), figure 2 from the Yang et al. paper lays it out quite clearly:

Let’s back up for a moment and set the stage. What did they do in the PNAS paper which claims that one can not reject the model that the Eurasian affinity to Neandertals is due to ancient African population structure (i.e., the African ancestors of Eurasians already had a closer affinity to Neandertals, perhaps due to continuous gene flow)? Basically they created an explicit spatial model with a temporal dimension. The authors simulated parameters of gene flow (and lack thereof) as well as bottlenecks, etc., and found that ancient structure easily generated the D-statistic which the original authors of the Neandertal admixture paper relied upon.

So why so dismissive from Reich & Patterson? Because the Yang et al. paper admits this problem, and formulates a way to test alternative scenarios which generate just those D-statistics, but exhibit different demographic histories. What they found in Yang et al. is that a model where a population bottleneck occurs followed by admixture is the best fit to the site frequency spectrum that you see in real populations today. In other words, they also simulated situations where ancient structure generated equivalent D-statistics to admixture, and then furthermore explored scenarios where other population genetic statistics could further prune the alternatives. One could say that the appropriate follow up paper to the PNAS contribution was actually published before it.

The paper on arXiv (to be published in PLoS Genetics) goes much further. Using patterns of the linkage disequilibrium in the genome they produce a date when the admixture occurred. The statistical genetics here is somewhat opaque to the casual reader, so interpretation of these results probably should be conditional on the Yang et al. paper, whose results are more elegant and easy to digest.

After all is said and done David Reich’s judgment is not atypical. Several people who I know personally and are deeply immersed in human population genomics are simply not impressed by the PNAS paper. That happens, and there’s no shame in it. But Reich has a point: a speedier process of publication and review would have saved a lot of people some energy.

Related: Dienekes’ comments.

  • http://dienekes.blogspot.com Dienekes

    The Yang et al. paper introduces African population structure by the window, because they claim that Eurasians and Yoruba split at 112.5ky and Eurasians admixed with Neandertals at 50ky.

    http://dienekes.blogspot.com/2012/04/neandertal-admixture-vs-ancient-african.html

    So, where were Eurasians hiding for 62.5ky, after they split off from Yoruba and before they supposedly expanded Out-of-Africa with “Upper Paleolithic” technologies to mix with Neandertals?

    Actually, Yoruba most emphatically did NOT split from Eurasians 112.5ky because the majority of their mtDNA and near 100% of their Y chromosomes belong to haplogroups L3 and DE respectively, that coalesce within the sub-70ka time frame.

    So, if Yoruba have common ancestors with Eurasians in the sub-70ka time period, and their “population divergence” (assuming a tree model) is 112.5ka, that can only mean one thing: that their sub-70ka ancestors mixed with pre-112.5ka Africans to produce something that averages out to 112.5ka.

    There you go: African population structure by the window.

    The new paper by the Reich lab does document (through LD-based methods) a plausible episode of gene flow between modern humans and Neandertals post-70ka, but does not really quantify what this amounts to, or indeed what was the direction of gene flow; they only consider SNPs with MAF less than 10%, i.e., recent SNPs.

    On the other hand, the D-statistic signal detected in the earlier paper did not use such a threshold. All SNPs, not only low-frequency ones were included.

    The jury is very much out on what fraction of the 2-4% “Neandertal admixture” detected by Green et al. represents genuine recent Neandertal admixture, what fraction represents modern-to-Neandertal admixture in the Vindija genome (http://dienekes.blogspot.com/2012/01/neandertal-shoulder-blades-and.html), and what fraction represents Neandertal-to-modern admixture.

  • dave chamberlin

    Patterson says “the allelic frequency spectrum of Neanderthal alleles in Eurasia falls off very quickly.”
    Dienekes says in his related comments you link to “neanderthals were a West Eurasian distributed species and yet there is no major excess of Neanderthal variation in Western Eurasions.”

    One comment comes close to contradicting the other. It takes someone more knowledgable than me to draw conclusions from the body of evidence to date as to whom is more likely to be right but it is a fascinating question that I hope Razib continous to report on which is the world wide distribution of archaic alleles in modern populations.

  • Nick Patterson

    Just a quick response, which will most likely be my last on this thread

    On 2) There’s no contradiction here. Dienekes is worried that there is not more Neandertal genetics in West Eurasia than E. Asia. Nothing to do with allelic spectrum.

    And in my opinion the date of Yoruba/Eurasian split is irrelevant. Most Neandertal genes have to have come into Eurasia after the out of Africa bottleneck. I see no way to fit that with ancient substructure as the explanation.

  • http://dienekes.blogspot.com Dienekes

    The Yoruba-Eurasian split is relevant in the context of Yang et al. because their model involves a Yoruba-Eurasian split at 112.5ky.

    There was no such split at 112.5ky, because mtDNA L3 coalesces to 70ka and includes virtually all Eurasian mtDNA and most Yoruba mtDNA, while Y-haplogroup CT coalesces to post-70ka, and includes virtually all Yoruba and Eurasian Y-chromosomes.

    So, there was no Yoruba-Eurasian split at 112.5ky: the two populations exchanged genes long after their supposed split. Indeed, the evidence is that the major part of Yoruba ancestry is shared with Eurasians within the last 70ka. So, what accounts for the 112.5ky date?

    Actually, the 112.5ky date comes from a paper by Li and Durbin which used a 2.5×10^-8 autosomal mutation rate and a recent human-chimp divergence date. But, now, thanks to the new human-chimp calibration and the direct measurements of the autosomal mutation rate (which is about half the previous value), this date must go up, A LOT.

    So, if Yoruba did not really split from Eurasians 112.5ky (or indeed, something like 200ky+ if the much earlier date necessitated by the direct mutation rate) but are a composite of two populations, the major one sharing common ancestry with Eurasians within the last 70ky, then what type of hominin did admix with to produce the average value of 112.5ky (or 200ky+)

    Answer: something a lot older than 200ky.

    In other words, the Yang et al. admixture model does not correspond to known population history.

    As for the evidence for recent introgression in the Sankararaman et al, paper, this applies to SNPs with less than 10% MAF in Europeans, i.e., recent SNPs. Some of these may involve Neandertal-to-modern gene flow (likely for the region detected by Mendez et al. in a paper that just came out), while others may involve modern-to-Vindija gene flow. (Vindijia is definitely post-modern arrival in Europe, and has a morphology consistent with modern-to-Neandertal gene flow).

  • Lank

    @Dienekes:

    Actually, Yoruba most emphatically did NOT split from Eurasians 112.5ky because the majority of their mtDNA and near 100% of their Y chromosomes belong to haplogroups L3 and DE respectively, that coalesce within the sub-70ka time frame.

    That’s right: There was no distinct proto-Yoruba group that split from proto-Eurasians >100 kya. Rather, the Yoruba descend from several groups, whose divergence with Eurasians vary by tens of thousands of years. One of these groups shares common ancestry with Eurasians in the OoA time frame (Y-DNA CT and mtDNA L3). But, it has always been clear on the mtDNA side that part of their ancestry is certainly more divergent. Of course, archaic admixture in Eurasians, and possibly West Africans as well (although this hasn’t been shown yet), should also influence results to some degree.

    On what are you basing that the majority of Yoruba mtDNA belongs to L3, anyway? This study sampled southeastern Nigerians and Ghanaians, neither of which are predominantly L3. Yoruba should be somewhere in between the two.

    As for where the L3 spread originated, East Africa is still the best candidate for many reasons. It is the place where L3 is most diverse. In fact, some of the L3 lineages that diverged quite early on, around 60 kya, are still virtually specific to East Africa (L3a, L3h). In addition, L3f and L3eikx seem to be more ancient in East Africa than anywhere else. This figure from “The Expansion of mtDNA Haplogroup L3 within and out of Africa” by Soares et al. sums things up fairly well, based on the current evidence.

    Y-DNA E likely spread into West Africa from East Africa, as most West African E lineages derive from lineages that likely originated in East Africa tens of thousands of years ago. For this reason, I believe that E1b1 may have spread into West Africa alongside the oldest L3 lineages found in this region (L3e, L3bd), around 40 kya, when Soares et al. identified a peak in the L3 effective population size. These E males were obviously very successful, which is why the more divergent lineages in the Y chromosome phylogeny are rarely found in modern West Africans. However, it seems that E carriers in both East Africa and West Africa didn’t venture into Central-Southern Africa with any success until far later, during the Bantu expansion and spread of pastoralism. Then again, it seems likely that some BT carriers may have expanded south from East Africa before E1b1 existed. The most common B subclade (B2b), which is found in hunter-gatherers from all over Africa, is most diverse in East African hunter-gatherers.

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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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