Any potential explanation would have to account for the fact that this happened around the world, not only in certain sub-populations. The article isn't clear on whether it began at different times in different places, possibly because the data isn't complete enough. A start date of 70,000 years ago suggests it has something to do with human exodus from africa that occurred around that time. The difficulty is that even southern africans see the change, suggesting that it wasn't particular to the emmigrees.
I would therefore propose that some event occurred which pushed humans out of africa, which lead to those that remained having smaller brains, and ultimately lead those that left to the same position. Perhaps that explanation is simply population density. Populations tend to expand geometrically, such that the largest portion of population growth occurs in the latest generations. We also know that all modern humans are descended from a very small set of people, maybe as few as fifty (?).
So humans began at that population, slowly expanded across africa for a few tens of thousand of years, started running out of space and were forced to migrate away from africa, then shortly filled up the rest of the earth. Having no where else to escape to, we were forced to deal with increased population density. This lead to lower food availability to support large brains, as well as increased need to reduce aggressive behaviour, achieved via more juvenile brains. Thus, brain sizes reduced across the globe.
The article makes reference to this phenomenon being global:
> Yuval Harari says that the worst choice in the history of human societies is when humans made the transition from nomadic hunter-gatherers to sedentary farmers. With this, humans became much more susceptible to malnutrition, disease, and famine. Their grain-heavy diets lacked critical nutrients that are essential to proper brain function. But, we see brain shrinkage in the aboriginal people of Australia and South Africans, who never succumbed to agriculture until recent times, and we see the same amount of shrinkage in these populations as well.
It's possible as you say that founder effects and reverse migration and interbreeding could account for this, but an alternative theory is that trade emerged as a driving force of human activity, incentivising new behaviours, and so ultimately it was memetics that changed the selection parameters that shrunk brain sizes
Another question not addressed in the article is whether the shrinkage is linear or happened in spurts (and if so, when these occurred). It's entirely possible, for example, that there was some shrinkage 60-70k years ago, then noting happened for 50k years, and then some more shrinkage in the last 10k years.
Another interesting tidbit not mentioned is that you can actually remove a full half of the brain of young children (hemispherectomy) and these people have very normal lives with extremely small or no impact on their brain functions, which is pretty bonkers. This underscores that size isn't everything.
I would therefore propose that some event occurred which pushed humans out of africa, which lead to those that remained having smaller brains, and ultimately lead those that left to the same position. Perhaps that explanation is simply population density. Populations tend to expand geometrically, such that the largest portion of population growth occurs in the latest generations. We also know that all modern humans are descended from a very small set of people, maybe as few as fifty (?).
So humans began at that population, slowly expanded across africa for a few tens of thousand of years, started running out of space and were forced to migrate away from africa, then shortly filled up the rest of the earth. Having no where else to escape to, we were forced to deal with increased population density. This lead to lower food availability to support large brains, as well as increased need to reduce aggressive behaviour, achieved via more juvenile brains. Thus, brain sizes reduced across the globe.