Questioning the level of modern human contamination in the Neandertal FOXP2 gene sequence

One of my favorite papers from last year was the investigation of FOXP2 allele in Neandertals. It seems like it was one of your favorite papers too, that post gets a lot of hits still! That being said, I think we’ll all appreciate a brand new paper (in works) on this specific topic. It was caught first by Dienekes, and then Razib.

The authors behind the new paper, “The Timing of Selection at the Human FOXP2 Gene,” don’t accept that the FOXP2 allele modern humans and Neandertals carry coulda originated over 300,000 years ago — in a shared common ancestor of both species. Instead, they wonder if the sequence similarity observed is attributed to low rates of gene flow between modern humans and Neandertals, or even contamination.

The issue of contamination was raised last year, at the same time by Sung Kim and Jeffrey Wall, but on a much larger scale… Sung Kim and Jeffrey Wall had beef with quality of the 1 million base pair sequence of Neandertals.

The authors of this new paper,

“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.”

I don’t have advance access to the manuscript, but from what I can read in the abstract, I know I’ll appreciate it a lot. Why? Well, I’ve personally been doing a lot of research on FOXP2 and know how conserved it is. There are very few differences in the sequence of FOXP2 alleles from chimps and humans, so there maybe even fewer differences in the sequence of FOXP2 alleles of other hominins to humans. The ways Neandertal fossils are collected, even in the most sterile conditions, could introduce modern human DNA that will alter conclusions and the fact that the authors of this new paper hone in on that, is something I look forward to reading.

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