RT Journal Article SR Electronic T1 The quantity of Neanderthal DNA in modern humans: a reanalysis relaxing the assumption of constant mutation rate JF bioRxiv FD Cold Spring Harbor Laboratory SP 065359 DO 10.1101/065359 A1 William Amos YR 2016 UL http://biorxiv.org/content/early/2016/07/27/065359.abstract AB Few now dispute that a few percent of the DNA of non-African humans is a legacy of interbreeding with Neanderthals. However, heterozygosity and mutation rate appear to be linked such that the loss of diversity associated with humans migrating out of Africa caused a mutational slowdown, allowing Africans to diverge more from both our common ancestor and Neanderthals. Here I use a range of contrasting tests aimed at distinguishing between mutation slowdown and introgression as explanations for the higher rates of base-sharing between non-Africans and Neanderthals. In every instance the mutation slowdown hypothesis fits better. Thus, while some interbreeding likely occurred, as evidenced by the finding of skeletons of admixed individuals, adaptive genes and the apparently large contribution of Denisovan DNA to Oceanian genomes, my results challenge the idea that non-Africans generally carry an appreciable Neanderthal legacy. My analysis shows that inferences about introgression may be unreliable unless variation in mutation rate linked to demographically induced changes in heterozygosity can be excluded as an alternative hypothesis.