Many allergies can be traced to lifestyle factors for which the sufferer has no evolutionary adaptation. Allergies are not the same as intolerances, but the following applies to both.
Lactose intolerance reflects the fact that humans have been consuming milk from cattle, goats, sheep, camels and other non-human animals for a maximum of 400 generations or about 0.2% of the duration of evolution of our distinct species. Many humans lose, in early/middle childhood, the ability to produce the enzyme most effective in lactose digestion. The same applies to gluten intolerance, reflecting the fact that, although humans have probably consumed grains for over two million years, until the Neolithic they did not farm grains and so did not eat them in sufficient quantities to adapt fully to them.
I am not aware of any published studies demonstrating that a Pleistocene diet can have a significant impact on the symptoms of these intolerances, but it certainly makes sense.
Tony McMichael addresses the question "Why has asthma increased seven-fold over the last 25 years?" He reports (pages 324-5) that some scientists think that this may largely reflect changes in family size and domestic environments that, in turn, have reduced early-life exposures to microbes and their effects. There would thus have been a generation-based change in the usual life pattern of early-life maturation of the human immune system. In particular, the traditional load of intestinal worms in childhood normally damps down the immune system's allergic response system by way of an adaptive response acquired by those parasites during their co-evolution with primates. As modern children in wealthy societies no longer undergo that suppressive process may explain an increasing allergic tendency that predisposes to asthma and other allergic disorders. Dietary changes may also contribute, particularly the reduced consumption of immune suppressive omega-3 fatty acids may also have influenced the pattern of allergic response in generations of children born in the 1960s through to the 1980s. The same phenomenon featured in the 2001 PBS television series "Evolution".
We can't go back to the mix of microbes with which our ancestors evolved, but we can help our long- and medium-term health by
• using antibiotics sparingly and always according to directions
• eating organic foods (grown without antibiotics)
• tolerating dirt, bacteria and mild illnesses as preferable to severe allergies and catastrophic infections and epidemics.