Recent direct measurement of the human mutation rate strongly suggest that it is about half as large as previously estimated. Neutral genetic differences between groups would have taken longer to accumulate.
Therefore, estimates of population splits need to be recalibrated. Generally, this suggests that everything in human prehistory happened considerably earlier than previously thought. For example, using the old value of the mutation rate, researchers had estimated that the split between modern humans and Neanderthals/Denisovans took place 272,000-435,000 years ago – which seemed odd at the time, since Europe has plenty of hominid fossils that look to be on their way to becoming Neanderthals, yet are considerably older than that split estimate. The new mutation estimates now fits the fossil evidence. Along the same lines, the previous estimate had modern humans exiting Africa about 60,000 years ago, which meant that the fairly-modern looking Skhul/Qafzeh, fossils found in Israel, some 80,000-120,000 years old, must have died out without contributing to modern Eurasians. Which was possible, of course, but not as simple and appealing as a single Out-of-Africa expansion. The revised mutation rate, along with recent evidence of an African middle stone age tool tradition (Nubian complex) in South Arabia, makes for a simpler story, one in which the Skhul/Qafzeh population eventually expanded into Eurasia.
But the story still isn’t all that simple, because we’ve never found
anatomically modern fossils that are more than 50k years old further out into Eurasia. Somehow, anatomically modern humans (AMH) didn’t yet have the moxie to displace archaic humans. They apparently spent tens of thousands years stuck in the Middle East.
Maybe that makes sense. We know that people outside sub-Saharan Africa have lower levels of genetic variation than Africans: maybe an extended stay in the southern Middle East could have that effect. Consider that the area habitable by early hunter-gatherers isn’t very big, at least during the desertification stages. The Sahara, and Neanderthals in the Levant, could have blocked gene flow with sub-Saharan Africa. That’s the scenario you need to reduce genetic variation: small numbers and isolation.
Why the lag? It may help to think of AMH as an invasive species. Very often, some new pest shows up and spends quite a while hanging around the point of origin, not yet seeming very formidable. At some point, it transitions into an irresistible menace, like crabgrass. Our best guess is that the budding pest species spends that lag time responding to selection, becoming better adapted to its new environment. Sometimes the newcomer manages to steal useful genes from related species, which naturally are already adapted to that environment. Starting with potential advantages over the locals, and now prepared for local conditions, the invasive species set forth to conquer.
You might also think of south Arabia as the wading pool, a place different from sub-Sahara Africa, but not too different. AMH needed to make some changes: lose expensive immunological defenses against African zoonoses, acquire the necessary defenses against Eurasian pathogens, begin to adjust to lower temperatures and more variation in the length of the day, etc.. Neanderthal admixture likely helped.
AMH really needed some kind of trump card: it is not easy to displace a competitor with similar abilities that’s already locally adapted. Although their toolkit is not yet much different from Neanderthals, the Skhul/Qafzeh population already showed some signs of greater cultural capabilities, like a ritual burial with grave goods. Somehow, though, that wasn’t enough – success against Neanderthals waited another 50,00o years.