Murray Cox and Michael Hammer have a short commentary piece in the current BMC Biology, titled, “A question of scale: Human migrations writ large and small”
It’s a short review, but I thought their conclusion serves some thought – they discuss some of the theoretical complexity of estimating ancient rates of gene flow. The simple model assumes constant rates, but human populations aren’t simple.
We expand on just one of these points for illustration (Figure 3). Even when gene flow is inferred explicitly, existing methods invariably assume that it has remained constant through time. However, it seems more reasonable that two diverging populations might share more migrants initially (due to shared geography or existing social relationships), with gene flow subsequently decreasing exponentially as the two populations move apart (Figure 3a). Or gene flow might increase exponentially as two geographically separated populations begin to move closer together (Figure 3b). Alternatively, gene flow might suddenly resume between two long separated populations; for instance, where geographically disconnected populations came back into contact, either as hunter-gatherer groups during the late Pleistocene (Figure 3d), or as human mobility increased following the development of farming in the Holocene (Figure 3c). The important point is this: two populations can look very similar (FST = 0) or very different (FST = 0.3) even when they have exchanged the same number of migrants (that is, graph lines with the same color in figure 3). It is therefore insufficient to consider only how many migrants have moved between populations; we also need to know when these movements occurred.
I don’t reproduce the figure, because it’s complicated and I think the text is sufficient to establish the point. Averages aren’t very meaningful. I’ll point out that there is some hope of testing these hypotheses, if we consider selected genes – which have a time that they originated.