So what’s point of demographic models which leave you scratching your head

There’s a new paper on Tibetan adaptation to high altitudes, Evolutionary history of Tibetans inferred from whole-genome sequencing. The focus of the paper is on the fact that more genes than have previously been analyzed seem to be the targets of natural selection. And I buy most of their analyses (not sure about the estimate of Denisovan ancestry being 0.4%…these sorts of things can be tricky).

But they fancy it up with a ∂a∂i model of population history, as well as using MSMC to account for gene flow. I don’t understand why they didn’t use something simpler like TreeMix, which can also handle more complex models. I guess because they wanted to focus on only a few populations?

Years ago I asked the developer of MSMC, Stephan Schiffels, if assuming an admixed population is not admixed might cause weird inferences. Why yes, it would. For example, admixed populations might show higher effective population since they’re pooling the histories of two separate populations. As for ∂a∂i, the model above leaves me literally scratching my head.

…predicted that the initial divergence between Han and Tibetan was much earlier, at 54kya (bootstrap 95% C.I 44 kya to 58 kya). However, for the first 45ky, the two populations maintained substantial gene flow (6.8×10-4 and 9.0×10-4 per generation per chromosome). After 9.4 kya (bootstrap 95% C.I 8.6 kya to 11.2 kya), the gene flow rate dramatically dropped (1.3×10-11 and 4×10-7 per generation per chromosome), which is consistent with the estimate from MSMC.

Mystifying. The separation between Chinese and Tibetans is pretty much immediately after modern humans arrive in East Asia. Then there’s a lot of reciprocal gene flow…which ends during the Holocene.

We’re being told here that there are two populations which persisted in some form for ~45,000 years. Is this believable? That these two populations maintained some sort of continuity, and, remained in close proximity to engage in gene flow. And then ~10,000 years ago the ancestors of the Tibetans separated from the ancestors of the modern Han Chinese.

The latter scenario I can imagine. It’s this ~45,000 year dance I’m confused by. If there is substantial gene flow between the two groups why did they keep enough distinctive drift to be separate populations?

With what we know about ancient DNA from Europe if we posited such a model for that continent we’d be way off. There’s been too many population turnovers. Is East Asia different? I’m moderately skeptical of that. I think perhaps researchers should be very aware of the limitations of ∂a∂i when it comes to fine-grained population genomic analyses.

Note: This is a cool paper, and this small section is not entirely relevant. Which is why I’m confused about it since it seems the weakest part of the analysis in terms of originality, and the least believable.

How Tibetans can function at high altitudes

About seven years ago I wrote two posts about how Tibetans manage to function at very high altitudes. And it’s not just physiological functioning, that is, fitness straightforwardly understood. High altitudes can cause a sharp reduction in reproductive fitness because women can not carry pregnancies to term. In other words, high altitude is a very strong selection pressure. You adapt, or you die off.

For me there have been two things of note since those original papers came out. First, one of those loci seem to have been introgressed from a Denisovan genetic background. I want to be careful here, because the initial admixture event may not have been into the Tibetans proper, but earlier hunter-gatherers who descend from Out of Africa groups, who were assimilated into the Tibetans as they expanded 5-10,000 years ago. Second, it turns out that dogs have been targeted for selection on EPAS1 as well (the “Denisovan” introgression) for altitude adaptation as well.

This shows that in mammals at least there’s a few genes which show up again and again. The fact that EPAS1 and EGLN1 were hits on relatively small sample sizes also reinforces their powerful effect. When the EPAS1 results initially came out they were highlighted as the strongest and fastest instance of natural selection in human evolutionary history. One can quibble about the details about whether this was literally true, but that it was a powerful selective event no one could deny.

A new paper in PNAS, Genetic signatures of high-altitude adaptation in Tibetans, revisits the earlier results with a much larger sample size (the research group is in China) comparing Han Chinese and Tibetans. They confirm the earlier results, but, they also find other loci which seem likely targets of selection in Tibetans. Below is the list:

SNP A1 A2 Frequency of A1 P value FST Nearest gene
Tibetan EAS (Han)
rs1801133 A G 0.238 0.333 6.30E-09 0.021 MTHFR
rs71673426 C T 0.102 0.013 1.50E-08 0.1 RAP1A
rs78720557 A T 0.498 0.201 4.70E-08 0.191 NEK7
rs78561501 A G 0.599 0.135 6.10E-15 0.414 EGLN1
rs116611511 G A 0.447 0.003 3.60E-19 0.57 EPAS1
rs2584462 G A 0.211 0.549 3.90E-09 0.203 ADH7
rs4498258 T A 0.586 0.287 1.70E-08 0.171 FGF10
rs9275281 G A 0.095 0.365 1.10E-10 0.162 HLA-DQB1
rs139129572 GA G 0.316 0.449 5.80E-09 0.036 HCAR2
P value indicates the P value from the MLMA-LOCO analysis. FST is the FST value between Tibetans and EASs. Nearest gene indicates the nearest annotated gene to the top differentiated SNP at each locus except EGLN1, which is known to be associated with high-altitude adaptation; rs139129572 is an insertion SNP with two alleles: GA and G. A1, allele 1; A2, allele 2.

Many of these genes are familiar. Observe the allele frequency differences between the Tibetans and other East Asians (mostly Han). The sample sizes are on the order of thousands, and the SNP-chip had nearly 300,000 markers. What they found was that the between population Fst of Han to Tibetan was ~0.01. So only 1% of the SNP variance in their data was partitioned between the two groups. These alleles are huge outliers.

The authors used some sophisticated statistical methods to correct for exigencies of population structure, drift, admixture, etc., to converge upon these hits, but even through inspection the deviation on these alleles is clear. And as they note in the paper it isn’t clear all of these genes are selected simply for hypoxia adaptation. MTFHR, which is quite often a signal of selection, may have something to due to folate production (higher altitudes have more UV). ADH7 is part of a set of genes which always seem to be under selection, and HLA is never a surprise.

Rather than get caught up in the details it is important to note here that expansion into novel habitats results in lots of changes in populations, so that two groups can diverge quite fast on functional characteristics.  The PCA makes it clear that Tibetans and Hans have very little West Eurasian admixture, and the Fst based analysis puts their divergence on the order of 5,000 years before the present. The authors admit honestly that this is probably a lower bound value, but I also think it is quite likely that Tibetans, and probably Han too, are compound populations, and a simple bifurcation model from a common ancestral population is probably shaving away too many realistic edges. In plainer language, there has been gene flow between Han and Tibetans probably <5,000 years ago, and Tibetans themselves probably assimilated more deeply diverged populations in the highlands as they expanded as agriculturalists. An estimate of a single divergence fits a complex history to too simple of a model quite often.

The take home: understanding population history is probably important to get a better sense of the dynamics of adaptation.

Citation: Jian Yang, Zi-Bing Jin, Jie Chen, Xiu-Feng Huang, Xiao-Man Li, Yuan-Bo Liang, Jian-Yang Mao, Xin Chen, Zhili Zheng, Andrew Bakshi, Dong-Dong Zheng, Mei-Qin Zheng, Naomi R. Wray, Peter M. Visscher, Fan Lu, and Jia Qu, Genetic signatures of high-altitude adaptation in Tibetans, PNAS 2017 ; published ahead of print April 3, 2017, doi:10.1073/pnas.1617042114