How do changes in habitat affect frequencies of phenotypes (features) in a species?

The frequencies of the phenotypes that impart survival advantage to the organisms under the changed conditions are increased by natural selection.  

Explanation:

Genetic variations are present in the natural population. Some genetic traits and the corresponding phenotypes become adaptive under the changed conditions. These organisms survive better and reproduce more successfully to leave more progeny. This results in an increase in the proportions of the beneficial phenotypes in the population over generations. For example, antibiotic resistance in the bacterial population increase when antibiotics are present in their surroundings.