Detecting ancient admixture and estimating demographic parameters in multiple human populations
I read this paper on our way back from Leipzig and then again today to see if I missed anything in the first read through (I was pretty tired at the time).
Detecting ancient admixture and estimating demographic parameters in multiple human populations
Wall, Lohmueller and Plagnol, Mol Biol Evo 26(8):1823-1827
We analyze patterns of genetic variation in extant human polymorphism data from the National Institute of Environmental Health Sciences single nucleotide polymorphism project to estimate human demographic parameters. We update our previous work by considering a larger data set (more genes and more populations) and by explicitly estimating the amount of putative admixture between modern humans and archaic human groups (e.g., Neandertals, Homo erectus, and Homo floresiensis). We find evidence for this ancient admixture in European, East Asian, and West African samples, suggesting that admixture between diverged hominin groups may be a general feature of recent human evolution.
What they do in this paper is to fit a two population coalescent model, with expansion, migration, bottlenecks and the works, to both an African+European and an African+Asian data set, then use this fitted model as a null model of the genetics of the populations. They then 1) do a test on an LD statistic against this null model, taking rejections of this null model as evidence for admixture from archaic humans, and 2) fit an admixture extension of the model to estimate the level of admixture. They find evidence for admixture with archaic humans for both data sets, with a somewhat higher degree in the Europeans.
I’m a bit underwhelmed by the paper, I must admit. I’m not saying that there is no admixture with archaic humans, but this approach does not convince me.
Even when taking various demographic effects into account in the modeling, the null model is unlikely to exactly fit real data. Taking deviations from the null model as any kind of evidence for admixture thus seems a bit hasty.
Not that I have any better ideas as to how to approach this, just, in my eyes the jury is still out on the question of admixture with archaic humans…
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Wall, J., Lohmueller, K., & Plagnol, V. (2009). Detecting Ancient Admixture and Estimating Demographic Parameters in Multiple Human Populations Molecular Biology and Evolution, 26 (8), 1823-1827 DOI: 10.1093/molbev/msp096
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September 26th, 2009 at 5:29 pm
I’m a bit underwhelmed by the paper, I must admit. I’m not saying that there is no admixture with archaic humans, but this approach does not convince me.
Yeah, that makes two of us. The way they set up their model, any departure from Wright-Fisher is going to make nonzero admixture a better fit than zero. There are lots of alternative population structure scenarios that could do this.
September 26th, 2009 at 5:35 pm
I agree completely. It just seems to unattractive to use deviations from a null model, that we don’t really expect to fit particularly well, as evidence for one particular scenario when the deviation could be explained by lots of other, equally likely, scenarios.