A relatively higher mutation rate in African humans is the dominant mechanism causing Neanderthals to appear closer to non-Africans, not introgression

It is widely thought that humans carry genetic legacies due to
inter-breeding with Neanderthals, but all methods used to infer legacies
ignore recurrent mutations and assume a constant mutation rate. These
assumptions cause automatic rejection of a second hypothesis, where a
higher mutation rate in Africans caused increased divergence from
Neanderthals. Any fair test should strive to treat both hypotheses
equally. Here I use mutation spectra, the relative frequencies of
different mutating three-base combinations, to compare contrasting
expectations from the two hypotheses. I find that putative introgressed
bases are strongly enriched for recurrent mutations and lie in regions
with unusually high mutation rates, distorted mutation spectra and
unusually large African minus non-African heterozygosity differences.
Moreover, putative introgressed bases should be absent from Africa and
rare outside, yet almost the entire signal of introgression is carried by
sites where putative Neanderthal alleles are fixed in non-Africans and at
high frequency in Africans. Together, these observations support a model
where signals of introgression are driven mostly or even entirely by
mutation rate differences between human populations. This new model helps
to explain why introgression is inferred ubiquitously, including in
scenarios involving great apes where inter-breeding is biologically
implausible.