Krause et al. (2007) recently examined patterns of genetic variation^ at FOXP2 in two Neandertals. This gene is of particular interest^ because it is involved in speech and language and was previously^ shown to harbor the signature of recent positive selection.^ The authors found the same two amino-acid substitutions in Neandertals^ as in modern humans. Assuming that these sites were the targets^ of selection and no interbreeding between the two groups, they^ concluded that selection at FOXP2 occurred before the populations^ split, over 300Kya. Here, we show that the data are unlikely^ under this scenario but may instead be consistent with low rates^ of gene flow between modern humans and Neandertals. We also^ collect additional data and introduce a modeling framework to^ estimate levels of modern human contamination of the Neandertal^ samples. We find that, depending on the assumptions, additional^ control experiments may be needed to rule out contamination^ at FOXP2.
Update: Kambiz has much more.