Offhand, I would think that an explanation would be that differences in geographic locations caused differences in genetics and these differences were then passed until today.
CT
Because of microevolution (i.e. genetic drift) the occurrence of small-scale changes in allele frequencies in a populations over time, accounts for differences. There are likewise documentable differences, for example, in susceptibility to certain diseases. Some races are more prone than others to certain illnesses and genetic disorders in other words.
Environment plays a role as well. Sustained abject poverty, which is coupled with serious malnutrition for a sizable populace over time, leads to deteriorating genetic quality and impaired brain development potential, which may take several generations to recover. It's a fact of life in the Third World.
Islands where cannibalism was practiced suffered immense genetic deterioration. It basically causes diseases analagous to mad cow disease when it goes on for generations.
For whatever reason sub-equatorial and sub-saharan peoples tend to have more developed lower body strength, leg muscles, etc. In contrast, those peoples whose bounds were in frigid or colder regions tended to be more rigid on top with sturdier frame, and ease in building upper body strength. These are just population observations where concentrations of these traits have been found more common, not absolutes or general rules.
The changes in our diet has actually increased the average heights of many people in Western industrialized world irrespective of race. Though, some think cures for childhood diseases which impaired growth play a part in the discrepency between Americans now and those 300 years ago. Others suggest hormones in beef.
Societies where life has harsh elements seems to have compeled people to more complex social organizations. How much of that is genetic or cultural remains debatable.
"And He hath made of one blood all nations of men for to dwell on all the face of the earth, and hath determined the times before appointed, and the bounds of their habitation."
Acts 17:26