Choosing a second option choice
Admissions committees have been in the business of matching grad students with classes and advisors for a long time. To provide the best fit, they have asked students for their specialization preference knowing that while some students are sure of their path (pure, applied, or statistics), others will change their mind with a broader exposure. Listing a second option should increase your chances of acceptance, for it gives the admissions committee more options.

While I cannot imagine an admissions committee penalizing students listing a secondary option, they will likely be displeased with wishy-washy students calling to change minor application details.