How do you know that most of the reason is nurture rather than nature?
If I recall correctly, Rushton's position was that most of the reason is nature, something like 60%.
I don't know whether it's possible to calculate how much is accounted for by nature or nurutre.
My theory is that populations are more similar than different (obviously), but there are slight general differences if you take the average in each population. The idea that we're all exactly the same on the inside even though we evolved to look differently on the outside flies in the face of evolutionary theory. Supposing populations continue to intermix, there will eventually be no ethnically distinct groups and this will become a non-issue. However, it will take thousands of years for that day to arrive.
Take each person on their individual merits and enjoy life.
The two obvious natural physical characteristics that goes with 'smarts', and many book on anthropology or physiology will back it up, is size of the brain and the number and complexity of neural pathways. They can go hand in hand as the bigger brain will generally have more pathways, but you can also increase the numbers and complexities of these pathways by exercising your brain, read studying, and practice. A person with brain damage can grow new pathways and learning/relearning functions and memories. Brain tissue dies just like tissue in the rest of the body and if you don't exercise it, replacement of these pathways will differ or not happen at all.
It's not a direct correlation, as in a person with a larger brain will be smarter, but the potential is there. In human evolution, the human race evolved and subsequent species had larger brains, from ~300 cc in Australopithecus to todays ~1500 cc in homo sapiens giving rise to increased potential for an in skills. Cro-Magnon's brain was 10/15% larger than modern man, but not as convoluted. I believe it was noticed after Einstein death that his brain was ~15% bigger than the normal human. The more complex brains will also have more creases. Another physical attributes is the different development of the different areas of the brain, giving rise to different strengths and weaknesses in certain skills such as languages, spacial acuity, problem, solving and such. The brain is generally symmetrical, but not perfectly so. Then growth of new pathways explained why young children learn so much so quickly especially when compared to later stages of life.
There are also correlation between species that involves brain chemicals and DNA adding to the complexity, but that's beyond my abilities to easily explain.
Add to that the better diet, emotional support, social pressures to succeed,increased access to learning materials and facilities and you increase that end result.