Testing an alternative explanation for relatively greater base-sharing between Neanderthals and non-African humans

Most accept that non-African humans share [~]2% of their genome with Neanderthals (1) and that inter-breeding occurred between several archaic lineages (2-4). However, most evidence assumes that mutation rate is constant. It has been suggested that heterozygosity is mutagenic (5-8). If so, an alternative explanation of the data becomes possible. Instead of non-Africans sharing relatively more bases with Neanderthals due to interbreeding, Africans could appear unexpectedly divergent due to their mutation rate not having been lowered when diversity was lost during the out of Africa bottleneck. I therefore tested a series of predictions aimed at distinguishing mutation slowdown from inter-breeding. Predictions from mutation slowdown are generally better supported. For example, the signal used to infer inter-breeding remains even when Neanderthal sequences are excluded. I conclude that, while some inter-breeding probably did occur, an appreciable component of the signal seems better explained by mutation slowdown.