There’s been a mild debate in the literature about the human mutation rate recently. I assume it will reach some consensus within the next few years, but until then Nature Reviews Genetics has published something which lays out the implications in precise fashion for a slower mutation rate. Revising the human mutation rate: implications for understanding human evolution:
The four key points may be summarized as follows. First, the divergence between modern humans and both Neanderthals and Denisovans, which was originally estimated to be 272,000–435,000 years ago, is revised to 400,000–600,000 years ago. This is in better agreement with the range of estimated split times from mtDNA and also with the idea that the ancestral population of these groups may have been H. heidelbergensis. Second, for the split between the Khoe–San and other modern humans, revised estimates from nuclear genomic data suggest a divergence 250,000–300,000 years ago, older than single-locus estimates for the root of the human tree. Third, revised estimates of the separation time between Africans and non-Africans suggest that this predates the appearance of modern humans in Europe and Asia by up to 60,000 years. We have suggested a scenario of exodus from Africa via an intermediate population in East Africa and the Middle East, which may fit better with growing evidence for modern human occupation of the latter region before the wider colonization of Eurasia and may provide a longer interval for Neanderthal admixture with non-African populations. Finally, revised split times of 40,000–80,000 years ago for Europeans and Asians agree better with the palaeoanthropological record and with estimates from mtDNA.
The authors do understand that their phylogenetic model impacts their inferences. If there was a lot of archaic admixture into the Khoe and Bushmen their divergence from other modern humans might be inflated. But it is always striking to me that there is this strange result that populations like the Yoruba might be in a clade with non-Africans against Khoe and Bushmen.