More comes to light about the function of the rhesus protein. One of its functions is to prevent the blood from becoming acidic. Another is oxygen transport. Could it have been that the first ever mutation of rh negative blood took place somewhere around sea level by the sea or ocean where more oxygen supply was granted?
See also:
The Structure and Function of the Rh antigen Complex
Rhesus factors and ammonium: a function in efflux?