Unexplained Allele-Calling Errors May Account for Apparent Denisovan-Neanderthal F1 Genome

The recent report that DNA extracted from ancient bone must have from the offspring of a female Neanderthal and a male Denisovan depends on the inference that the subject has a high level of heterozygosity for Neanderthal and Denisovan alleles across the genome. Here I point out that the relative frequencies of derived transversion polymorphisms varies markedly between the new specimen, Denisova 11, and two high-coverage Neanderthal genomes. In Denisova 11 the AC and CG polymorphisms are much commoner than the others and are almost twice as common as the AT polymorphism. In the high-coverage Neanderthal genomes the four types of transversion are about equally common, with the AT being slightly commoner than the others. These results suggest that allele-calling errors are frequent and that this may provide an alternative explanation for the observed heterozygosity.