There are both social and physical issues with Native Americans and alcoholism as far as root causes go. Because of a number of complex social factors including a generational loss of identity, extreme poverty and unemployment (which leads to higher rates of alcoholism in any population) and a shorter historical experience with alcohol, some argue that Native Americans have a greater predisposition towards alcoholism.
We need to treat that assertion with some care, however, as predisposition does not mean genetic inevitability. The Native experience with Europeans is just over five centuries long, with some tribes (such as the Plains tribes) having a much briefer period of contact with settlers and therefore less exposure to alcohol.
As the theory of evolution goes with this topic, Europeans had been exposed to alcohol use for thousands of years by the time the first Native tribes were introduced to it, meaning that Europeans who could not tolerate alcohol died out and those who built a tolerance reproduced, creating a population of Europeans more able to resist alcoholism. The trouble with that is there is almost no way to prove it, it just seems to make evolutionary sense.
We also need to be careful of assuming the problems with alcohol found on some reservations automatically can be found on every reservation, or with every Indian. This simply perpetuates an inaccurate and damaging stereotype.