To me, Diamond is not really saying that there is a major barrier that divides all of Africa from Eurasia. Instead, there is a major barrier that separates central and southern Africa from northern Africa and Eurasia. That barrier is the Sahara Desert.
Diamond talks in this chapter about how that barrier prevented the spread of crops and domesticated animals (the tsetse fly helped with the animals) from Eurasia and northern Africa down into the rest of the continent. This is the real split -- not the split between Africa as a whole and Eurasia.