On 2014 Apr 23, Janet Kelso commented:

We, the authors of the Neandertal genome papers, are not aware of any modern human contamination over and above that which is clearly quantified and reported in our manuscripts. We have developed and published a number of approaches to quantify modern human contamination using both mitochondrial and nuclear sequence data (Green RE, 2008, Green RE, 2009, Meyer M, 2012, Prüfer et al., 2013). In each paper where we report DNA sequences from archaic humans we have carefully quantified and reported any modern human contamination detected. As we have said in responsee to previous similar comments, it is difficult to respond to rumors without knowing the substance of the analyses on which such rumors are based. We would be interested to see the data and analyses that suggest modern human contamination in the in excess of that reported in the published Neandertal genome manuscripts.

On 2014 Feb 24, Steven Salzberg commented:

These authors identified human variants that matched the Neandertal reference genome, and used this as the basis (in part) for identifying extensive evidence of Neandertal remnants in modern humans. However, I have heard recently, from geneticists working in the area, that some of the published Neandertal sequences contain human contaminants, despite the efforts of the Paabo group to keep such contaminants out. If so, then building additional conclusions such as this paper on the "Neandertal" edifice might turn out to be a house of cards. I think more work is needed to ascertain that sequences published as Neandertal are truly free of modern human sequences.

On 2014 Feb 17, Reinhard Stindl commented:

Vernot et al. discovered over 15 Gb of introgressed Neandertal sequence in modern humans, but only 23 Mb of introgressed sequence per individual (on average). Very interesting results indeed! Surprisingly, no modern human sequences have been found in genome drafts of Neandertals despite the claim of multiple hybridizations. Green RE, 2010 Wills C, 2011 It remains to be seen, if other Neandertal sequencing projects will discover genetic remnants of hybridizations with modern humans. If not, the current model of human evolution is in trouble. The multiregional model with local Neandertals directly transforming into modern humans might better explain the extreme variation of inherited Neandertal sequences in modern human populations and the absence of any modern human genetic sequence in Neandertal DNA.

On 2014 Feb 17, Reinhard Stindl commented:

Vernot et al. discovered over 15 Gb of introgressed Neandertal sequence in modern humans, but only 23 Mb of introgressed sequence per individual (on average). Very interesting results indeed! Surprisingly, no modern human sequences have been found in genome drafts of Neandertals despite the claim of multiple hybridizations. Green RE, 2010 Wills C, 2011 It remains to be seen, if other Neandertal sequencing projects will discover genetic remnants of hybridizations with modern humans. If not, the current model of human evolution is in trouble. The multiregional model with local Neandertals directly transforming into modern humans might better explain the extreme variation of inherited Neandertal sequences in modern human populations and the absence of any modern human genetic sequence in Neandertal DNA.