Models are great, because rejection is easy

There’s a new paper in PLoS ONE, Female and Male Perspectives on the Neolithic Transition in Europe: Clues from Ancient and Modern Genetic Data, which uses a combination of contemporary and ancient (that is, from subfossils) Y and mitochondrial DNA to understand the demographic past of Europe. Recall that the Y traces the direct male lineage, and the mtDNA the direct female lineage. Because they don’t recombine and generate clean converges back to a last common ancestor (there is no reticulation because there is no sex on these loci; they’re inherited from one of the two parents), they’re amenable to a lot of nifty demographic inference generation. In this paper they test specific models, and produce probability distributions of those models. Since it is open access I invite you to read the paper. The problem with these sorts of papers is I have a hard time trusting them until I replicate the results or have a sense of how cranky the software/code is!

But there’s a bigger problem. The authors find that ~80% of Spanish ancestry is “Paleolithic” and ~100% of that of Southeast Europeans is “Neolithic.” I don’t have a problem with these figures so much, except that autosomal DNA generally implies the major genetic cline in Europe is north-south, not east-west! By this, I mean that there is more variation between Poland and Greece, than Greece and Spain, and Spain and England, than Spain and Greece. At least on the whole genome scale. But this tends not to be the case when you look at Y chromosomes, for example. There’s an east-west split. Why? I have no idea, but the fact of this contradiction exists should make you cautious.

Finally, I have to throw in that it seems that this model is focused on one expansion of farmers into Europe. Though reading structure plots can be like reading tea-leaves, I think it is important to enter into the record that this may not be correct, and there may have been multiple agricultural expansions. If so, I wonder about the validity of the inferences if the assumptions are faulty. These are all things one has to consider when one tries to gauge the plausibility of abstruse statistical papers like this dependent on silico

Citation: Rasteiro R, Chikhi L (2013) Female and Male Perspectives on the Neolithic Transition in Europe: Clues from Ancient and Modern Genetic Data. PLoS ONE 8(4): e60944. doi:10.1371/journal.pone.0060944

Source: Discover Magazine – Gene Expression